I don’t know if this will make a difference, but I believe it is generally
preferred to use the poly() function (for lm()/glm()) or the pol() function
(for rms functions) to include the quadratic (and higher order terms).
Kevin
> On Feb 18, 2025, at 12:23 PM, Ben Bolker <bbol...@gmail.com> wrote:
>
> Looking at the 'contrasts' function, it seems to be imported from 'rms' and
> to take only 'rms'-type fits (which are different from base-R [g]lm() fits)
> as input.
>
> I'm not sure exactly what contrasts you're trying to generate, but I would
> probably use the emmeans package for the task, since it handles a wide range
> of model types.
>
> Alternately, you could use one of the modeling functions from rms, which
> should work with rms::contrast(), although I ran into trouble for some reason:
>
> fit1 <- ols(y ~ x + I(x^2), data = mydata)
>
> > Error in if (!length(fname) || !any(fname == zname)) { :
> missing value where TRUE/FALSE needed
>
> I guess rms handles I()-protected terms differently? (The model with just y~x
> didn't throw an error ...)
>
> On 2025-02-18 12:00 p.m., Sorkin, John wrote:
>> I am using the contrast package to produce contrasts from a glm model that
>> contains a quadratic term:
>> fit0 <- glm(y ~ x + I(x*x),data=mydata)
>> I would like to know how to specify the quadratic term, I(x*x), in the
>> contrast function.
>> When I try to use
>> contrast(fit0,list(x=4))
>> I receive an error message;
>> #Error in generateData(fit = list(coefficients = c(`(Intercept)` =
>> 0.5262645536229, :not enough factors
>> When I try to use
>> contrast(fit0,list(x=4,I(x*x)=16))
>> I receive an error message:
>> #Error: unexpected '=' in "contrast(fit0,list(x=4,I(x*x)="
>> Other variants of the call to contrast including
>> contrast(fit0,list(x=4,"x*x"=16)) and
>> contrast(fit0,list(x=4,"I(x*x}"=16))
>> produce similar error messsages.
>> Please see my code below.
>> if (!require(contrast)) install.packages("contrast")
>> library(contrast)
>> help(contrast)
>> x <- 1:100
>> y <- x + x^2 + rnorm(1)
>> mydata <- data.frame(x=x,y=y)
>> fit0 <- glm(y ~ x + I(x*x),data=mydata)
>> summary(fit0)
>> contrast(fit0,list(x=4))
>> #Error in generateData(fit = list(coefficients = c(`(Intercept)` =
>> #0.5262645536229, : not enough factors
>> contrast(fit0,list(x=4,I(x*x)=16))
>> #Error: unexpected '=' in "contrast(fit0,list(x=4,I(x*x)="
>> Thank you,
>> John
>> ______________________________________________
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>> PLEASE do read the posting guide https://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> --
> Dr. Benjamin Bolker
> Professor, Mathematics & Statistics and Biology, McMaster University
> Director, School of Computational Science and Engineering
> > E-mail is sent at my convenience; I don't expect replies outside of working
> > hours.
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide https://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Kevin E. Thorpe
Associate Professor, Dalla Lana School of Public Health
University of Toronto, Tel: 416-946-8083
Scientific Lead, Clinical Trials Design and Analysis, Hospital for Sick Children
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